Chapter 130 Molecular epidemiology of viral infections

Molecular epidemiology is the integration of epidemiology, the study of the distribution and risk factors of disease, and molecular biology, the study of biological diversity and processes at the molecular level. In the context of viral infections, applications of molecular epidemiology predominantly focus on characterizing variation in the nucleic acid molecule(s) that comprise the virus genome. This chapter, will review the fundamental concepts and recent progress in the molecular epidemiology of viral infections. It will start with the use of genetic sequences to catalog the diversity of viruses, how we can map this diversity to the global distribution of the virus, and identify statistical associations between genetic variation and clinical variables. Next, it will explore topics on emerging viral infections, including the discovery of new viruses, and the use of probabilistic models to reconstruct the origin and spread of a virus in recent history. This chapter will examine how similar methods are used to reconstruct the transmission history of viral infections and identify risk factors associated with transmission risk. Finally, it will discuss how the analysis of viral sequences sampled from a given patient is used to study the pathogenesis and host-specific adaptation of the virus.